Development of a quantitative model for comparing the genomic and epidemiological signal of foodborne pathogens : improving the application of whole-genome sequencing to infectious disease epidemiology

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dc.contributor.authorHetman, Benjamin M.
dc.contributor.authorUniversity of Lethbridge. Faculty of Arts and Science
dc.contributor.supervisorThomas, James E.
dc.contributor.supervisorTaboada, Eduardo N.
dc.date.accessioned2016-05-24T17:36:07Z
dc.date.available2016-05-24T17:36:07Z
dc.date.issued2016
dc.degree.levelMastersen_US
dc.description.abstractInterpreting microbial whole genome sequencing data remains an ongoing challenge in the fields of public health and epidemiology. For this thesis, 274 isolates of the human bacterial pathogen Campylobacter jejuni were selected for sequencing on the basis of their genotype and sampling metadata. A novel core genome typing method revealed that the genomic signal of bacterial isolates is not always concordant with their underlying epidemiology. To systematically examine this relationship, I developed an analytical model for quantifying the epidemiological similarity of bacterial isolates based on their sampling metadata, allowing for direct comparison to their genomic similarities. Applying this model to my dataset highlighted certain genotypes that were present throughout several diverse ecologies in disproportionately high amounts. A competitive recovery experiment revealed that particular genotypes seen in high prevalence in national and international repositories display preferential growth under laboratory conditions, providing evidence for systematic bias in infectious disease surveillance systems.en_US
dc.embargoNoen_US
dc.identifier.urihttps://hdl.handle.net/10133/4486
dc.language.isoen_CAen_US
dc.proquest.subject0410en_US
dc.proquest.subject0715en_US
dc.proquest.subject0766en_US
dc.proquestyesYesen_US
dc.publisherLethbridge, Alta : University of Lethbridge, Dept. of Biological Sciencesen_US
dc.publisher.departmentDepartment of Biological Sciencesen_US
dc.publisher.facultyArts and Scienceen_US
dc.relation.ispartofseriesThesis (University of Lethbridge. Faculty of Arts and Science)en_US
dc.subjectbacterial isolatesen_US
dc.subjectCampylobacter jejunien_US
dc.subjectdisease surveillance systemsen_US
dc.subjectsystemic biasen_US
dc.subjectwhole genome sequenceen_US
dc.titleDevelopment of a quantitative model for comparing the genomic and epidemiological signal of foodborne pathogens : improving the application of whole-genome sequencing to infectious disease epidemiologyen_US
dc.typeThesisen_US
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